BOND-PEP: topology-conditioned bipartite alignment for evidence-grounded peptide binder generation

Abstract Peptide binders can modulate proteins that remain challenging for small molecules, but discovering high-affinity, selective peptides is still slow and sample-intensive. Sequence-first generators could scale design when structures are unavailable or conformationally heterogeneous, yet they often trade diversity for control: unconstrained sampling is inefficient while conditioning remains largely implicit. This limitation is exacerbated by the uneven transfer of protein language model priors to short peptides. Here we present BOND-PEP, a retrieval-augmented, bipartite-aligned, topology-conditioned framework that converts empirical binding evidence into an explicit, residue-resolved conditioning state for peptide generation. BOND-PEP shows low perplexity together with satisfactory free-generation hit rates and sequence novelty under a fair evaluation protocol and decoding budget. Compared with existing peptide generation methods, BOND-PEP achieves state-of-the-art results that match or improve upon validated peptide-protein sequence pairs. In total, BOND-PEP provides a practical, sequence-only route to controllable de novo peptide binder generation under noisy labels and distribution shift.